- Volume 53, Issue 1, 2003
Volume 53, Issue 1, 2003
- Validation List No. 89
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Validation of publication of new names and new combinations previously effectively published outside the IJSEM
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described previously [Int J Syst Bacteriol 27(3), iv (1977)]. Authors and other individuals wishing to have new names and/or combinations included in future lists should send the pertinent reprint or a photocopy thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination. T1
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- Notification List
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Notification that new names and new combinations have appeared in volume 52, part 5, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute II(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein have priority according to the page number of the IJSEM on which they were proposed. T1
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- New Taxa
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- Other Bacteria
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Marinithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney
More LessA novel thermophilic marine bacterium, designated strain T1T, was isolated from a deep-sea hydrothermal vent chimney sample collected from the Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1385 m. Cells of strain T1T were rod-shaped, occurring in pairs or filamentous, and stained Gram-negative. Growth was observed between 50·0 and 72·5 °C (optimum 67·5 °C; 30 min doubling time) and at pH 6·25–7·75 (optimum pH 7·00). The isolate absolutely required NaCl, at a concentration of 0·5–4·5 % (optimum 3·0 %). It was a strictly aerobic heterotroph capable of growing solely on complex organic substrates such as yeast extract, tryptone and Casamino acids, utilizing glutamate, proline, serine, cellobiose, trehalose, sucrose, acetate and pyruvate as complementary substrates. The G+C content of the genomic DNA was 68·6 mol%. The 16S rRNA gene sequence of the isolate was most similar to those from members of the genus Thermus, but the isolate was distantly related to them at the genus level (<90 %). In addition, phylogenetic analysis indicated that the isolate was on a novel lineage, deeply branched prior to divergence of the genus Thermus. On the basis of phylogenetic analysis and physiological traits of the isolate, it should be described as a member of a novel genus distinct from the previously described genus Thermus. The name Marinithermus gen. nov. is proposed, with Marinithermus hydrothermalis gen. nov., sp. nov. as the type species. The type strain of M. hydrothermalis gen. nov., sp. nov. is strain T1T (=JCM 11576T =DSM 14884T).
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Reichenbachia agariperforans gen. nov., sp. nov., a novel marine bacterium in the phylum Cytophaga–Flavobacterium–Bacteroides
More LessA heterotrophic, pigmented, agarolytic, gliding bacterium was isolated from a seawater sample collected from the Gulf of Peter the Great, Sea of Japan, during June 2000. 16S rDNA sequence analysis indicated that the novel bacterium, strain KMM 3525T, was a member of the phlyum Cytophaga–Flavobacterium–Bacteroides. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, it is proposed that the marine bacterium represents the sole species of a novel genus, Reichenbachia, the type species of which is Reichenbachia agariperforans (KMM 3525T =IFO 16625T =JCM 11238T).
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Chryseobacterium defluvii sp. nov., isolated from wastewater
More LessA Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterium (strain B2T) isolated from wastewater of a sequence batch reactor showing enhanced phosphorus removal was investigated to determine its taxonomic status. Complete 16S rRNA gene sequence analysis indicated that the organism should be placed in the genus Chryseobacterium. The strain contained a polyamine pattern with sym-homospermidine as the major compound, menaquinone MK-6 as the predominant menaquinone and ai-C15 : 0, i-C15 : 0 and C16 : 1 as the major fatty acids. Phosphatidylethanolamine and several unidentified lipids were detected in the polar lipid profile. Phylogenetically, strain B2T was most closely related to Chryseobacterium indoltheticum and Chryseobacterium gleum (96·2 and 95·9 % 16S rRNA gene sequence similarity, respectively). The phylogenetic distance from any validly described species within the genus Chryseobacterium, as indicated from 16S rRNA gene sequence similarities, and its phenotypic properties demonstrate that strain B2T represents a novel species, for which the name Chryseobacterium defluvii sp. nov. is proposed; the type strain is B2T (=DSM 14219T =CIP 107207T).
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Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces
More LessA novel strictly anaerobic, cellobiose-degrading bacterium, strain CelloT, was isolated from a human faecal sample by combining enrichments in liquid and soft-agar basal media. A noteworthy characteristic was its inability to grow on normal agar plates and in roll tubes. The cells were coccus shaped and non-motile, with an extracellular slime layer. Growth of strain CelloT occurred between 20 and 40 °C, with optimal growth at 37 °C. The pH range for growth was 5–7·5 with an optimum at 6·5. In pure culture, strain CelloT could only grow on a variety of sugars. Glucose was converted to acetate, ethanol and H2. The doubling time on glucose was 0·5 h. In a syntrophic co-culture with Methanospirillum hungatei strain JF-1T, strain CelloT converted glucose to acetate and H2. The G+C content was 59·2 mol%. 16S rDNA analysis revealed that the closest relatives of strain CelloT were two uncultured bacteria from anaerobic digesters, both with 94 % 16S rDNA sequence similarity. The closest cultured representatives belong to genera of the bacterial division ‘Verrucomicrobia’. The name Victivallis vadensis gen. nov., sp. nov. is proposed for strain CelloT (=DSM 14823T =ATCC BAA-548T).
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Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage
A novel, moderately thermophilic, strictly anaerobic, mixotrophic bacterium, designated strain LF13T, was isolated from a deep-sea hydrothermal chimney sample that was collected at a vent site at 14° 45′ N, 44° 59′ W on the Mid-Atlantic Ridge. Cells were Gram-negative, thin, non-motile rods of variable length. Strain LF13T grew optimally at pH 6·8–7·0 and 60 °C with 2·5 % (w/v) NaCl. It grew chemo-organoheterotrophically, fermenting proteinaceous substrates, pyruvate and Casamino acids. The strain was able to grow by respiration, utilizing molecular hydrogen (chemolithoheterotrophically) or acetate as electron donors and nitrate as an electron acceptor. Ammonium was formed in the course of denitrification. One-hundred milligrams of yeast extract per litre were required for growth of the strain. The G+C content of the genomic DNA of strain LF13T was 42·5 mol%. Neither 16S rDNA sequence similarity values nor phylogenetic analysis unambiguously related strain LF13T with members of any recognized bacterial phyla. On the basis of 16S rDNA sequence comparisons, and in combination with physiological and morphological traits, a novel genus, Caldithrix, is proposed, with strain LF13T (=DSM 13497T =VKM B-2286T) representing the type species, Caldithrix abyssi.
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- Proteobacteria
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Bosea eneae sp. nov., Bosea massiliensis sp. nov. and Bosea vestrisii sp. nov., isolated from hospital water supplies, and emendation of the genus Bosea (Das et al. 1996)
More LessOn the basis of phenotypic and DNA relatedness data, three novel species of the genus Bosea are proposed, Bosea massiliensis (63287T =CIP 106336T =CCUG 43117T), Bosea vestrisii (34635T =CIP 106340T =CCUG 43114T) and Bosea eneae (34614T =CIP 106338T =CCUG 43111T). The original description of the genus Bosea included thiosulphate oxidation as a phenotypic feature, when the sole and type species of the genus, Bosea thiooxidans, was proposed. The three novel species described herein were not able to oxidize thiosulphate; thus, it is proposed that this characteristic be removed from the description of the genus and considered as specific for B. thiooxidans. The novel species of the genus Bosea proposed here form a well-separated cluster in the Bradyrhizobium group of the α-2 subclass of the Proteobacteria, on the basis of 16S rDNA gene sequence analysis. However, 16S rDNA gene sequence analysis was not sufficient to delineate the species; hence, DNA–DNA relatedness and phenotypic data were also required. All of the novel species described in this study are fastidious bacteria isolated from a hospital water supply, using co-cultivation with amoebae. This group of bacteria are hypothesized to be a potential cause of nosocomial infections. For treatment of infections caused by these novel bacteria, doxycycline appears to be the sole antibacterial compound with a consistently low MIC value.
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Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea
Among Pseudomonas strains isolated from Korean agricultural soils, four strains (Ps 9-14 group: Ps 1-2, Ps 1-10, Ps 5-5 and Ps 9-14T) from the Suwon, Goesan and Samchok regions, three strains (Ps 3-10 group: Ps 2-22, Ps 3-1 and Ps 3-10T) from Umsong Region and four strains (Pss 26 group: Pss 14, Pss 25, Pss 26T and Pss 27) from Jinju Region were identified as three independent groups on the basis of 16S rDNA sequence analysis. While, on the basis of 16S rDNA sequence analysis, Ps 9-14T and Ps 3-10T form a phyletic line with Pseudomonas jessenii CIP 105274T, ‘Pseudomonas pavonaceae’ IAM 1155 and Pseudomonas graminis DSM 11363T, Pss 26T is grouped with Pseudomonas citronellolis ATCC 13674T and Pseudomonas nitroreducens IAM 1439T. According to DNA–DNA hybridization studies, strain Ps 9-14T shows high DNA relatedness to strain Ps 3-10T (52 %) and Pseudomonas migulae CIP 105470T (49 %) and strain Ps 3-10T reveals high relatedness to strain Ps 9-14T (48 %) and P. jessenii CIP 105274T (45 %). Strain Pss 26T shows high relatedness to P. citronellolis LMG 18378T (54 %), P. nitroreducens ATCC 33634T (48 %) and Pseudomonas aeruginosa LMG 1242T (48 %). On the basis of phenotypic and genotypic analyses, three novel species of the genus Pseudomonas are proposed: Pseudomonas koreensis sp. nov. (type strain Ps 9-14T =LMG 21318T =KACC 10848T) for the Ps 9-14 group, Pseudomonas umsongensis sp. nov. (type strain Ps 3-10T =LMG 21317T =KACC 10847T) for the Ps 3-10 group and Pseudomonas jinjuensis sp. nov. (type strain Pss 26T =LMG 21316T =KACC 10760T) for the Pss 26 group.
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Porphyrobacter cryptus sp. nov., a novel slightly thermophilic, aerobic, bacteriochlorophyll a-containing species
More LessTwo strains of a novel aerobic, bacteriochlorophyll a-containing species of the α-4 subclass of the Proteobacteria were isolated from the hot spring at Alcafache in central Portugal. 16S rRNA gene sequence-based phylogenetic analyses showed the two novel isolates to be phylogenetically related to members of the genera Erythrobacter, Erythromicrobium and Porphyrobacter. The strains produce reddish-orange-pigmented colonies, have an optimum growth temperature of about 50 °C and could be distinguished from the species Porphyrobacter tepidarius, which also has a high growth temperature, primarily on the basis of the fatty acid composition. The novel species does not grow anaerobically in the presence or absence of a light source. The strains of the novel species utilize several single carbon sources for growth, most of which are also used by P. tepidarius. The species status of strains ALC-2T and ALC-3 was confirmed by low reassociation values of the DNA with species of the genera Erythrobacter, Erythromicrobium and Porphyrobacter. Phenotypic characteristics and 16S rRNA gene sequence analyses also show that strains ALC-2T (=DSM 12079T =ATCC BAA-386T) and ALC-3 (=DSM 12080) represent a novel species, for which the name Porphyrobacter cryptus sp. nov. is proposed.
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Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo
An oestradiol-degrading bacterium isolated at a sewage treatment plant in Tokyo was studied phenotypically, genotypically and phylogenetically. Analysis of its 16S rDNA sequence, DNA base composition, whole-cell fatty acid profile and isoprenoid quinone composition, as well as the presence of sphingoglycolipid, revealed that the isolate is a member of the genus Novosphingobium. However, the sequence similarity of its 16S rDNA to those of known Novosphingobium species was no higher than 97 %, implying that the isolate is distinctive. The results of DNA–DNA hybridization experiments and physiological characterization also indicated that the isolate represents a novel Novosphingobium species, for which the name Novosphingobium tardaugens sp. nov. is proposed; strain ARI-1T (=JCM 11434T =ATCC BAA-531T =IFO 16725T) is the type strain.
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Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh
More LessA Gram-negative, non-motile, non-spore-forming, moderately halophilic rod (strain SM-1T) was isolated from salt marsh around the junction of the Youngsan River and the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. This organism grew optimally at 37 °C and was able to grow at 10 and 45 °C. It grew optimally in the presence of 2–3 % (w/v) NaCl. The major fatty acids in strain SM-1T were iso-C15 : 0 and C16 : 0. Strain SM-1T and Microbulbifer hydrolyticus DSM 11525T were characterized by having ubiquinone-8 as the predominant respiratory lipoquinone. The DNA G+C content of strain SM-1T was 59 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain SM-1T formed a coherent cluster with M. hydrolyticus; this relationship was supported by a bootstrap resampling value of 100 %. The level of 16S rDNA identity between strain SM-1T and the type strain of M. hydrolyticus was 98·6 %. The mean level of DNA–DNA relatedness between strain SM-1T and the type strain of M. hydrolyticus was 20·6 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic data, strain SM-1T should be placed in the genus Microbulbifer as a member of a novel species, for which the name Microbulbifer salipaludis sp. nov. is proposed. The type strain of the novel species is strain SM-1T (=KCCM 41586T =JCM 11542T).
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Legionella busanensis sp. nov., isolated from cooling tower water in Korea
More LessThree Legionella-like micro-organisms, isolated from cooling tower water of a building in Busan, Korea, were characterized by a variety of biochemical and molecular phylogenetic tests. Analyses of whole-cell fatty acids and results of biochemical tests revealed that these three isolates are distinct from previously described Legionella species. Furthermore, results of comparative analyses of 16S rDNA (1476–1488 bp), mip (408 bp) and rpoB (300 bp) sequences also confirmed that these strains represent a novel species within the genus Legionella. The 16S rDNA sequences of the three Korean isolates had similarities of less than 95·8 % to other Legionella species. Phylogenetic trees formed by analysis of the 16S rRNA, rpoB and mip genes revealed that the isolates formed a distinct cluster within the genus Legionella. Based on the evaluated phenotypic and phylogenetic characteristics, it is proposed that these Korean isolates from water be classified as a novel species, Legionella busanensis sp. nov.; the type strain is strain K9951T (=KCTC 12084T =ATCC BAA-518T).
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‘Candidatus Glomeribacter gigasporarum’ gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi
More LessArbuscular mycorrhizal fungi are obligate endosymbionts that colonize the roots of almost 80 % of land plants. The present paper describes morphological and molecular data on a bacterial endosymbiont living in the cytoplasm of dormant or germinating spores and symbiotic mycelia of the fungal species Gigaspora margarita, Scutellospora persica and Scutellospora castanea. PCR amplification of almost the entire 16S rRNA gene of the Gigaspora margarita BEG 34 endosymbiont, using universal bacterial primers, and subsequent sequence analysis demonstrated that this organism occupies a very distinct phylogenetic position within the β-Proteobacteria, with the genera Burkholderia, Pandoraea and Ralstonia as its closest neighbours. Primers specific to the 16S rDNA of the endosymbiotic bacteria of BEG 34 allowed amplification of spore DNA from endosymbionts of Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea, but not from the Gigaspora gigantea endosymbiont (which was morphologically different) or from the cytoplasm of Gigaspora rosea (which did not contain endosymbiotic bacteria). These specific primers were successfully used as a probe for the in-situ hybridization of endobacteria in Gigaspora margarita spores. The overall rod-shaped morphology of the Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea endosymbionts was similar, and amplification and sequence analysis of the almost-complete 16S rRNA genes of several Gigaspora margarita, S. persica and S. castanea endosymbionts revealed over 98 % sequence similarity. These morphological and genomic characteristics were used to assign the endosymbionts of these three species (five isolates) of arbuscular mycorrhizal fungi as ‘Candidatus Glomeribacter gigasporarum’ gen. nov., sp. nov.
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Pseudoalteromonas agarivorans sp. nov., a novel marine agarolytic bacterium
The phenotypic, genomic and phylogenetic characteristics of four aerobic, Gram-negative, non-fermentative, motile, non-pigmented, agarolytic Pseudoalteromonas-like bacteria, isolated from marine environments, have been investigated. These bacteria share DNA–DNA similarities above 86 %. Comparative 16S rDNA sequence analysis of strain KMM 255T revealed its membership of the genus Pseudoalteromonas; it shares 99·9 % sequence similarity with Pseudoalteromonas distincta, Pseudoalteromonas elyakovii, Pseudoalteromonas atlantica and Pseudoalteromonas espejiana. DNA–DNA reassociation levels obtained for strain KMM 255T and type strains of these four species and other Pseudoalteromonas species were below 45 %. The marine isolates differed from known species of the genus by the fact that the cells are motile by means of a single flagellum or two to four polar unsheathed flagella and by an inability to utilize most organic compounds. On the basis of phenotypic, DNA–DNA hybridization and phylogenetic data, it is concluded that the isolates represent a novel species within the genus Pseudoalteromonas, for which the name Pseudoalteromonas agarivorans sp. nov. is proposed. The type strain is strain KMM 255T (=DSM 14585T).
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Alicycliphilus denitrificans gen. nov., sp. nov., a cyclohexanol-degrading, nitrate-reducing β-proteobacterium
More LessA facultatively denitrifying bacterium, strain K601T, was isolated at 30 °C from a municipal sewage plant on cyclohexanol as sole carbon source and nitrate as electron acceptor. Under aerobic conditions this strain used acetate, fumarate, lactate, pyruvate, crotonate, indole, glucose, vanillate, 4-hydroxybenzoate, m-cresol, o-cresol and p-cresol. Under denitrifying conditions the strain used cyclohexanol, cyclohexanone, 1,3-cyclohexanedione, 2-cyclohexenone, 1,3-cyclohexanediol (cis and trans), monocarboxylic acids (C2–C7), adipate, pimelate, 5-oxocaproate, citrate, 2-oxoglutarate, succinate, malate, crotonate, lactate, pyruvate and fumarate. Cells were short rods, 0·6 μm wide and 1–2 μm long, motile, non-spore-forming, Gram-negative, and catalase- and oxidase-positive. Strain K601T used nitrate, nitrite and oxygen as electron acceptors, but not sulfate, sulfite or fumarate. The DNA G+C content of strain K601T was 66 mol%. Phylogenetic analysis, based on 16S rDNA sequencing, showed that strain K601T represents a separate lineage of the family Comamonadaceae in the β-subclass of Proteobacteria. Based on the high 16S rDNA sequence divergence and phenotypic characteristics, the name Alicycliphilus denitrificans gen. nov., sp. nov. is proposed for this strain. The type strain is K601T (=DSM 14773T =CIP 107495T).
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Isolation and characterization of spirilloid purple phototrophic bacteria forming red layers in microbial mats of Mediterranean salterns: description of Halorhodospira neutriphila sp. nov. and emendation of the genus Halorhodospira
Microbial mats developing in the hypersaline lagoons of a commercial saltern in the Salin-de-Giraud (Rhône delta) were found to contain a red layer fully dominated by spirilloid phototrophic purple bacteria underlying a cyanobacterial layer. From this layer four strains of spirilloid purple bacteria were isolated, all of which were extremely halophilic. All strains were isolated by using the same medium under halophilic photolithoheterotrophic conditions. One of them, strain SG 3105 was a purple non-sulfur bacterial strain closely related to Rhodovibrio sodomensis with a 16S rDNA sequence similarity of 98·8 %. The three other isolated strains, SG 3301T, SG 3302 and SG 3304, were purple sulfur bacteria and were found to be very similar. The cells were motile by a polar tuft of flagella. Photosynthetic intracytoplasmic membranes of the lamellar stack type contained BChl a and spirilloxanthin as the major carotenoid. Phototrophic growth with sulfide as electron donor was poor; globules of elemental sulfur were present outside the cells. In the presence of sulfide and CO2 good growth occurred with organic substrates. Optimum growth occurred in the presence of 9–12 % (w/v) NaCl at neutral pH (optimal pH 6·8–7) and at 30–35 °C. The DNA base composition of strains SG 3301T and SG 3304 were 74·5 and 74·1 mol% G+C, respectively. According to the 16S rDNA sequences, strains SG 3301T and SG 3304 belonged to the genus Halorhodospira, but they were sufficiently separated morphologically, physiologically and genetically from other recognized Halorhodospira species to be described as a new species of the genus. They are, therefore, described as Halorhodospira neutriphila sp. nov. with strain SG 3301T as the type strain (=DSM 15116T).
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Desulfovibrio hydrothermalis sp. nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents
Mesophilic, hydrogenotrophic, sulfate-reducing bacteria were isolated from a deep-sea hydrothermal chimney sample collected at 13° N on the East-Pacific Rise at a depth of 2600 m. Two strains (BL5 and H9) were found to be phylogenetically similar to Desulfovibrio profundus (similarity >99 %), whereas two other strains (H1 and AM13T) were found to be phylogenetically distinct (similarity 96·4 %) from Desulfovibrio zosterae, their closest relative. Strain AM13T was characterized further. It was a barophilic, Gram-negative, non-sporulating, motile, vibrio-shaped or sigmoid bacterium possessing desulfoviridin. It grew at temperatures ranging from 20 to 40 °C, with an optimum at 35 °C in the presence of 2·5 % NaCl. The pH range for growth was 6·7–8·2 with an optimum around 7·8. Strain AM13T utilized H2/CO2, lactate, formate, ethanol, choline and glycerol as electron donors. Electron acceptors were sulfate, sulfite and thiosulfate, but not elemental sulfur or nitrate. The G+C content of DNA was 47 mol%. Strain AM13T (=DSM 14728T =CIP107303T) differed from D. zosterae not only phylogenetically, but also genomically (DNA–DNA reassociation value between the two bacteria was 23·8 %) and phenotypically. This isolate is therefore proposed as the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio hydrothermalis sp. nov.
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Reclassification of ‘Blastobacter viscosus’ 7d and ‘Blastobacter aminooxidans’ 14a as Xanthobacter viscosus sp. nov. and Xanthobacter aminoxidans sp. nov.
More LessOn the basis of morphological, physiological and genotypic properties ‘Blastobacter viscosus’ 7d and ‘Blastobacter aminooxidans’ 14a are proposed as new species of the genus Xanthobacter, Xanthobacter viscosus (type strain 7dT =VKM B-2253T =ATCC BAA-298T) and Xanthobacter aminoxidans corrig. (type strain 14aT =VKM B-2254T =ATCC BAA-299T).
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Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan
More LessTwo strains of a novel myxobacterium (designated SIR-1T and SHI-1) were isolated from Japanese coasts located in the Pacific subtropical zone. Cells of both strains were Gram-negative, rod-shaped and motile by gliding. The strains were chemoheterotrophic and strictly aerobic. They had the common characteristics associated with myxobacteria, such as bacteriolytic action and fruiting-body formation. The characteristic feature of the strains was a NaCl growth requirement with an optimum concentration of 2·0–3·0 % (w/v), comparable to that of sea water. In addition, other cationic components of sea water, such as Mg2+, Ca2+ and K+, were needed for growth. The major respiratory quinone was MK-8(H2). The cellular fatty acid profile was characterized by the predominance of iso-C15 : 0. Characteristic fatty acids anteiso-C16 : 0 and anteiso-C17 : 0, and a long-chain polyunsaturated fatty acid (C20 : 4), were also detected. The G+C content of the genomic DNA of strains SIR-1T and SHI-1 was between 69·3 and 70·0 mol% (as determined by HPLC). Strains SIR-1T and SHI-1 shared almost identical 16S rDNA sequences, and clustered with the genus Nannocystis as their closest relative upon phylogenetic analysis. However, the phylogenetic distance between the novel strains and the genus Nannocystis was large enough to warrant their different generic allocation. This finding was supported by significant phenotypic differences between the novel strains and Nannocystis. Thus, strains SIR-1T and SHI-1 represent a novel genus and species, for which the names Plesiocystis and Plesiocystis pacifica, respectively, are proposed. The type strain of the species is SIR-1T (=JCM 11591T =DSM 14875T =AJ 13960T).
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Methylophaga alcalica sp. nov., a novel alkaliphilic and moderately halophilic, obligately methylotrophic bacterium from an East Mongolian saline soda lake
More LessA moderately haloalkaliphilic and obligately methylotrophic bacterium (strain M39T) with the ribulose monophosphate pathway of carbon assimilation is described. Cells of this methanol and methylamine utilizer are aerobic, Gram-negative, asporogenous, motile short rods, multiplying by binary fission. It is auxotrophic for vitamin B12 and requires NaHCO3 or NaCl for growth in alkaline medium. Its cellular fatty acid profile consists primarily of straight-chain saturated C16 : 0 and unsaturated C16 : 1 and C18 : 1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol is also present. Optimal growth conditions are 25–29 °C, pH 9·0–9·5 and 3–4 % (w/v) NaCl. Cells accumulate the cyclic amino acid ectoine as the main compatible solute. The DNA G+C content is 48·3 mol%. Based on 16S rDNA sequence analysis and DNA–DNA relatedness (25–30 %) with the type strains of marine methylotrophs belonging to the genus Methylophaga, the novel isolate M39T (=VKM B-2251T =ATCC BAA-297T) was classified as the type strain of Methylophaga alcalica sp. nov.
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Paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium
A comprehensive taxonomic re-evaluation was performed on the marine, zeaxanthin-producing bacterium formerly classified as [Flavobacterium] sp. strain R-1512 (ATCC 21588). This strain, together with two other previously described marine isolates, [Flavobacterium] strain R-1506 and Paracoccus sp. strain MBIC 3966, were found to comprise a new species of the genus Paracoccus. The name Paracoccus zeaxanthinifaciens sp. nov. is proposed, with ATCC 21588T (=R-1512T =LMG 21293T) designated as the type strain.
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Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis
More LessFive Gram-negative bacterial strains, oxidase-positive, motile by means of more than one polar flagella, facultative anaerobe, arginine dihydrolase-negative, lysine- and ornithine decarboxylase-positive, sensitive to the vibriostatic agent O/129, were isolated from a flow-through rotifer culture system in Gent, Belgium, and previously characterized by fluorescent amplified fragment length polymorphism. Comparison of the 16S rDNA sequence of strain LMG 21460T indicated close relationships (∼99 % similarity) to Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus and Vibrio parahaemolyticus. However, DNA hybridization experiments revealed similarity values below 70 % with its closest species V. campbellii and V. harveyi. Additionally, the analysed strains differ from related Vibrio species by the utilization of melibiose and production of acid from l-arabinose and amygdalin. Among the strains analysed, differences were observed in some phenotypic characters, particularly susceptibility to ampicillin, polymyxin B and amikacin, and urease activity. The major fatty acids identified were 16 : 0, 18 : 1ω7c, 14 : 0, 12 : 0 3-OH and 18 : 0. Vibrio rotiferianus sp. nov. is proposed, with type strain LMG 21460T (=CAIM 577T); it has a DNA G+C content of 44·5±0·01 mol%.
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Vibrio neptunius sp. nov., Vibrio brasiliensis sp. nov. and Vibrio xuii sp. nov., isolated from the marine aquaculture environment (bivalves, fish, rotifers and shrimps)
The fluorescent amplified fragment length polymorphism (FAFLP) groups A5 (21 isolates), A8 (6 isolates) and A23 (3 isolates) distinguished in an earlier paper (Thompson et al., Syst Appl Microbiol 24, 520–538, 2001) were examined in more depth. These three groups were phylogenetically related to Vibrio tubiashii, but DNA–DNA hybridization experiments proved that the three AFLP groups are in fact novel species. Chemotaxonomic and phenotypic analyses further revealed several differences among the 30 isolates and known Vibrio species. It is proposed to accommodate these isolates in three novel species, namely Vibrio neptunius (type strain LMG 20536T; EMBL accession no. AJ316171; G+C content of the type strain 46·0 mol%), Vibrio brasiliensis (type strain LMG 20546T; EMBL accession no. AJ316172; G+C content of the type strain 45·9 mol%) and Vibrio xuii (type strain LMG 21346T; EMBL accession no. AJ316181; G+C content of the type strain 46·6 mol%). These species can be differentiated on the basis of phenotypic features, including fatty acid composition (particularly 14 : 0 iso, 14 : 0 iso 3-OH, 16 : 0 iso, 16 : 0, 17 : 0 and 17 : 1ω8c), enzyme activities and utilization and fermentation of various carbon sources.
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Spore-forming Serratia marcescens subsp. sakuensis subsp. nov., isolated from a domestic wastewater treatment tank
More LessA strain (KREDT) that formed endospores and produced the pigment prodigiosin was isolated from activated sludge. The presence of spores in cells of strain KREDT was evident upon electron microscopy examination, heat treatment and the detection of dipicolinic acid in the cells. Biochemical characteristics, and 16S rDNA sequence and DNA–DNA homology data identified strain KREDT as Serratia marcescens. The major respiratory quinone of strain KREDT was found to be ubiquinone Q-8. The formation of endospores by Gram-negative bacteria has not been observed previously, and has never been reported in any species of Serratia. Here, it is shown that strain KREDT (JCM 11315T=CIP 107489T) represents a novel subspecies of S. marcescens, for which the name Serratia marcescens subsp. sakuensis is proposed.
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Genetic relationships among avian isolates classified as Pasteurella haemolytica, ‘Actinobacillus salpingitidis’ or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov.
More LessBacteria of the avian [Pasteurella haemolytica]–‘Actinobacillus salpingitidis’ complex have been associated with different pathological conditions in birds, among which salpingitis and peritonitis in chickens of layer type seem to dominate. The aim of this study was to classify these bacteria by comparison of 37 strains tentatively classified as biovars of the avian [P. haemolytica]–‘A. salpingitidis’ complex or as Pasteurella anatis. PFGE, AFLP and plasmid profiling showed that strains representing different biovars were genotypically different. Phylogenetic analysis of 22 strains characterized by 16S rRNA gene sequence comparison showed that strains classified as biovars 5, 8 and 9 were closely related to the suggested type strain of ‘A. salpingitidis’ (98·4–99·9 % similarity), whereas the remaining strains classified in 12 biovars or as P. anatis were closely related to the type strain of P. anatis (98·1–100 % similarity). The two groups were related at 95·7–97·1 % similarity. The closest similarity outside this group was 94·6 %, between biovar 15 and Bisgaard taxon 3. DNA–DNA hybridization was performed with 34 strains and showed binding above 85 % for strains of biovars 5 and 8, including the suggested type strain of ‘A. salpingitidis’. Two strains of P. anatis (F 149T and F 279) were closely related at 79 % DNA binding to 27 strains of biovars 1, 3, 4, 11, 12, 17–20, 22 and 24. A new genus, Gallibacterium gen. nov., is proposed to include the avian [P. haemolytica]–‘A. salpingitidis’–P. anatis complex, since these taxa form a monophyletic unit with similarities above 95 % on the basis of 16S rRNA sequence comparison and they are unrelated to other genera of the family Pasteurellaceae Pohl 1981. The new genus consists of Gram-negative, non-motile, rod-shaped or pleomorphic bacteria. The bacteria are catalase-, oxidase- and phosphatase-positive. Nitrate is reduced and acid is produced without gas formation from glycerol, (−)d-ribose, (+)d-xylose, (−)d-mannitol, (−)d-fructose, (+)d-galactose, (+)d-glucose, (+)d-mannose, sucrose and raffinose. The genus Gallibacterium can be separated from other genera of Pasteurellaceae by differences in catalase, symbiotic growth, haemolysis, urease, indole, acid production from (+)d-xylose, (−)d-mannitol, (−)d-sorbitol, (+)d-mannose, maltose, raffinose and dextrin and ONPG and PNPG tests. Pasteurella anatis Mutters et al. 1985 is transferred to the new genus as Gallibacterium anatis gen. nov., comb. nov. Genomospecies 1 of Gallibacterium is proposed to include the former biovars 5 and 8 of the avian [P. haemolytica]–‘A. salpingitidis’ complex. The type strain of Gallibacterium anatis is F 149T (=ATCC 43329T=NCTC 11413T) and the reference strain of Gallibacterium genomospecies 1 is CCM 5974.
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Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis
More LessVibrio sp. YB1T (=ATCC BAA-450T =LMG 20984T), the aetiological agent of tissue lysis of the coral Pocillopora damicornis, was characterized as a novel Vibrio species on the basis of 16S rDNA sequence, DNA–DNA hybridization data (G+C content is 45·6 mol%), AFLP and GTG5-PCR genomic fingerprinting patterns and phenotypic properties, including the cellular fatty acid profile. The predominant fatty acids were 16 : 0 and 18 : 1ω7c. The name Vibrio coralliilyticus sp. nov. is proposed for the novel coral-pathogenic species. In addition to strain YB1T, which was isolated from the Indian Ocean, five additional strains of V. coralliilyticus have been isolated, three from diseased P. damicornis in the Red Sea, one from diseased oyster larvae (Kent, UK) and one from bivalve larvae (Brazil). The six V. coralliilyticus strains showed high genotypic and phenotypic similarities and all were pathogenic to P. damicornis. The closest phylogenetic neighbours to V. coralliilyticus are Vibrio tubiashii, Vibrio nereis and Vibrio shilonii.
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Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax
Two strains of a novel bacterium were isolated independently of each other, from different depths in the Mediterranean Sea, within a time period of 7 months, using two different isolation approaches that were focused on different objectives. Both strains, designated ISO1 and ISO4T, were halophilic, Gram-negative, strictly aerobic, straight rods that were oxidase- and catalase-positive. Both strains produced mucoid colonies in some defined minimal media and were able to grow with organic acids and some alkanes; they were also able to accumulate intracellular poly-β-hydroxybutyrate granules. The G+C content of the DNA of strain ISO4T was 66 mol%. Comparative analysis of 16S rRNA gene sequences showed that the closest described species to the novel strains were Alcanivorax borkumensis and Fundibacter jadensis, both of the γ-Proteobacteria. Both of these recognized species were originally isolated from North Sea waters and are able to degrade aliphatic compounds, a property shared with strains ISO1 and ISO4T. However, strains ISO1 and ISO4T were different from A. borkumensis and F. jadensis, not only in their 16S rDNA sequences but also in the motility of their cells (by polar flagella) and by the presence of C19 : 0cyclo in their cellular fatty acids, among other differential features. On the basis of biochemical and molecular data, it is suggested that strains ISO1 and ISO4T be recognized as a novel species of the genus Alcanivorax, for which the name Alcanivorax venustensis (ISO4T =DSM 13974T =CECT 5388T) is proposed. On the basis of its high phenotypic similarity and close phylogenetic relatedness to A. borkumensis, it is also proposed that F. jadensis (DSM 12178T) be reclassified as Alcanivorax jadensis in the genus Alcanivorax, and that the description of the genus Alcanivorax be emended.
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- Gram-Positive Bacteria
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Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.
More LessGenotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of dl-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G+C content was 37·5±0·2 mol%. The peptidoglycan was of the lysine–d-iso-asparagine (l-Lys–d-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA–DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).
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Nocardia cerradoensis sp. nov., a novel isolate from Cerrado soil in Brazil
An isolate from Cerrado soil, provisionally assigned to the genus Nocardia, was shown to have chemical and morphological properties typical of nocardiae. The strain formed a distinct monophyletic clade in the 16S rDNA tree together with Nocardia africana, Nocardia vaccinii and Nocardia veterana, and showed a unique combination of phenotypic properties that distinguished it from representatives of all recognized species of Nocardia. DNA–DNA relatedness studies indicated that the isolate belongs to a genomic species that is readily distinguished from its nearest neighbours, the type strains of N. africana and N. veterana. The organism is considered to merit species status, and it is proposed that it be designated Nocardia cerradoensis sp. nov., with strain Y9T (=CCT 5601T =DSM 44546T) as the type strain.
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Corynebacterium spheniscorum sp. nov., isolated from the cloacae of wild penguins
Twenty unidentified Gram-positive, rod-shaped organisms were recovered from the cloacae of apparently healthy wild penguins (Spheniscus magellanicus) and subjected to a polyphasic taxonomic analysis. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Corynebacterium, although the organisms did not appear to correspond to any recognized species. Lipid studies confirmed this generic placement, and comparative 16S rRNA gene sequencing showed that the unidentified organisms represent a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium diphtheriae and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from penguins be classified in the genus Corynebacterium, as Corynebacterium spheniscorum sp. nov. The type strain is strain PG 39T (=CCUG 45512T =CECT 5986T).
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Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra)
A bacterial strain, designated XIL07T, isolated from a decayed tree, Ulmus nigra, in Salamanca (Spain) produced abundant cellulases and xylanases. The micro-organism was Gram-positive, aerobic, coccoid and non-motile. Growth was observed on many carbohydrates, including cellulose and xylan as the sole carbon sources. No growth was observed with acetate, citrate, gluconate, inositol, malate or mannitol as carbon sources. The strain showed very weak catalase activity. HPLC analysis of menaquinones revealed two peaks: the main peak corresponded with MK-9(H4) and the smaller one with MK-8(H4). The major fatty acid found was anteiso-C15 : 0 (12-methyl tetradecanoic acid). Mycolic acids were absent. The polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. Peptidoglycan type was A4α, l-Lys–d-Asp. The cell-wall sugars detected were galactose and rhamnose. The complete 16S rDNA sequence of strain XIL07T was obtained and phylogenetic analysis based on the neighbour-joining method indicated that this bacterium belongs to the high-G+C-content Gram-positive bacteria and that the closest related genera are Promicromonospora and Cellulosimicrobium. The DNA G+C content was 73 mol%. According to the data obtained in this work, this bacterium belongs to a new genus in the family Promicromonosporaceae and the name Xylanimonas cellulosilytica gen. nov., sp. nov. is proposed; the type strain is strain XIL07T (=LMG 20990T =CECT 5975T).
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Lactobacillus ingluviei sp. nov., isolated from the intestinal tract of pigeons
More LessLactic acid bacteria were isolated from the crop and intestines of pigeons. One group of strains, showing similar genomic patterns after screening with tRNA intergenic spacer PCR, could not be identified to the species level. Sequencing of the 16S rRNA gene of one representative strain revealed about 96 % similarity to sequences from Lactobacillus fermentum and Lactobacillus mucosae. Determination of the DNA base composition, DNA–DNA hybridization experiments, SDS-PAGE of whole-cell proteins and biochemical testing confirmed that the seven strains studied constitute a single novel Lactobacillus species, for which the name Lactobacillus ingluviei sp. nov. is proposed. The type strain is strain KR3T (=LMG 20380T =CCUG 45722T).
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Actinomadura catellatispora sp. nov. and Actinomadura glauciflava sp. nov., from a sewage ditch and soil in southern China
Two soil isolates, strains 80-60T and 3.24T, were shown to have chemical and morphological properties consistent with their classification in the genus Actinomadura. The almost complete 16S rDNA sequences generated for the two organisms were aligned with available sequences of representatives of the genus Actinomadura and related taxa. It was apparent from the resultant phylogenetic trees that each of the strains formed a distinct phyletic line within the evolutionary radiation occupied by the genus Actinomadura. The two organisms could also be distinguished from one another and from representatives of all the validly described species of Actinomadura using a set of phenotypic properties. It is proposed that strains 3.24T (=AS 4.1522T =IFO 16341T) and 80-60T (=AS 4.1202T =IFO 14668T =JCM 16161T) be classified in the genus Actinomadura as Actinomadura catellatispora sp. nov. and Actinomadura glauciflava sp. nov., respectively.
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Emended description of Streptococcus ferus isolated from pigs and rats
Streptococcus ferus is a mutans-like streptococcus originally isolated from wild rats fed with sugar cane. Taxonomically, this species has not been studied extensively. Ten Gram-positive coccal strains, isolated from the tonsils and nasal conchae of piglets, were identified as S. ferus by 16S rDNA sequencing, tRNA-intergenic spacer length polymorphism analysis (tDNA-PCR), whole-cell protein profiling using SDS-PAGE, G+C content determination and extensive biochemical testing. In all these tests, the type strain of S. ferus (LMG 16520T), from a rat, was included. The results of the tests are described and an emended species description is presented.
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Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are γ-radiation resistant
More LessOne of the spore-formers isolated from a spacecraft-assembly facility, belonging to the genus Bacillus, is described on the basis of phenotypic characterization, 16S rDNA sequence analysis and DNA–DNA hybridization studies. It is a Gram-positive, facultatively anaerobic, rod-shaped eubacterium that produces endospores. The spores of this novel bacterial species exhibited resistance to UV, γ-radiation, H2O2 and desiccation. The 16S rDNA sequence analysis revealed a clear affiliation between this strain and members of the low G+C Firmicutes. High 16S rDNA sequence similarity values were found with members of the genus Bacillus and this was supported by fatty acid profiles. The 16S rDNA sequence similarity between strain FO-92T and Bacillus benzoevorans DSM 5391T was very high. However, molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in this genus, but DNA–DNA hybridization data support the proposal of FO-92T as Bacillus nealsonii sp. nov. (type strain is FO-92T =ATCC BAA-519T =DSM 15077T).
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Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample
Strain CMS 76orT, an orange-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. On the basis of chemotaxonomic and phylogenetic properties, strain CMS 76orT was identified as a member of the genus Kocuria. It exhibited a 16S rDNA similarity of 99·8 % and DNA–DNA similarity of 71 % with Kocuria rosea (ATCC 186T). Phenotypic traits confirmed that strain CMS 76orT and K. rosea were well differentiated. Furthermore, strain CMS 76orT could be differentiated from the other reported species of Kocuria, namely Kocuria kristinae (ATCC 27570T), Kocuria varians (ATCC 15306T), Kocuria rhizophila (DSM 11926T) and Kocuria palustris (DSM 11025T), on the basis of a number of phenotypic features. Therefore, it is proposed that strain CMS 76orT (=MTCC 3702T =DSM 14382T) be assigned to a novel species of the genus Kocuria, as Kocuria polaris.
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‘Candidatus Pasteuria usgae’ sp. nov., an obligate endoparasite of the phytoparasitic nematode Belonolaimus longicaudatus
Taxonomically relevant characteristics of a fastidiously Gram-positive, obligately endoparasitic prokaryote (strain S-1) that uses the phytoparasitic sting nematode Belonolaimus longicaudatus as its host are reviewed. 16S rDNA sequence similarity (⩾93 %) confirms its congeneric ranking with other Pasteuria species and strains from nematodes and cladocerans and corroborates morphological, morphometric and host range evidence suggesting a novel taxon. The 16S rDNA sequence of strain S-1 has greatest similarity (96 %) to the 16S rDNA sequences of both Pasteuria penetrans from root-knot nematodes (Meloidogyne species) and the recently reported strain of Pasteuria isolated from the soybean cyst nematode Heterodera glycines. Because the obligately endoparasitic nature of prokaryotes in the genus Pasteuria prevents isolation of definitive type strains, strain S-1 is proposed as ‘Candidatus Pasteuria usgae’ sp. nov.
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Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen
More LessTwo novel Gram-negative, anaerobic, non-spore-forming, butyrate-producing bacterial species, strains Mz 5T and JK 615T, were isolated from the rumen fluid of cow and sheep. Both strains were curved rods that were motile by means of single polar or subpolar flagellum and common in the rumen microbial ecosystem. Strain Mz 5T produced high xylanase, proteinase, pectin hydrolase and DNase activities; 1,4-β-endoglucanase was also detected in the culture medium. The bacterium utilized a wide range of carbohydrates. Glucose was fermented to formate, butyrate, lactate, succinate and ethanol. The DNA G+C content was 42·1 mol%. The complete 16S rDNA sequence was obtained and phylogenetic relationships were determined. Strain Mz 5T and related isolates were located in clostridial cluster XIVa and were closely related to Pseudobutyrivibrio ruminis, Butyrivibrio crossotus, Roseburia cecicola and Eubacterium rectale. The name proposed for this novel bacterium is Pseudobutyrivibrio xylanivorans; the type strain is Mz 5T (=DSM 14809T =ATCC BAA-455T). Strain JK 615T produced no fibrolytic activity, but utilized a wide range of carbohydrates. Glucose was fermented to formate, acetate, butyrate and ethanol. The DNA G+C content was 44·8 mol%. The complete 16S rDNA sequence was obtained and phylogenetic relationships were determined. Strain JK 615T was located in clostridial cluster XIVa and was closely related to Clostridium proteoclasticum, Butyrivibrio fibrisolvens and Eubacterium halii. The name proposed for this novel bacterium is Butyrivibrio hungatei; the type strain is JK 615T (=DSM 14810T =ATCC BAA-456T).
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Streptomyces yunnanensis sp. nov., a mesophile from soils in Yunnan, China
More LessA strain was isolated from red soil from the suburb of Kunming in Yunnan, China, during the screening of agricultural antibiotics which prevented and cured wheat-stem rust. This isolate, designated YIM 41004T (=CGMCC 4.1004T =DSM 41793T), was identified by a polyphasic approach. The test results suggested that this strain was clearly assigned to the genus Streptomyces and found to be marginally close to Williams cluster 32 based on the morphological and physiological data. The almost-complete 16S rRNA gene sequence of the strain was determined and compared with those of representative streptomycetes. The phylogenetic tree confirmed its membership in the genus Streptomyces and demonstrated that this strain represented a separate phyletic line in a clade encompassed by streptomycetes within cluster 32. Based on the polyphasic evidence, it is therefore proposed that strain YIM 41004T should be classified as Streptomyces yunnanensis sp. nov.
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Clostridium colicanis sp. nov., from canine faeces
Morphological, biochemical and molecular genetic studies were performed on an unknown, anaerobic, rod-shaped organism isolated from faeces of a canine. The organism was tentatively identified as a member of the genus Clostridium based on its cellular morphology and ability to form endospores but, biochemically, it did not appear to correspond to any recognized species of this genus. Comparative 16S rRNA gene sequence analysis showed that the bacterium represents a previously unrecognized subline within Clostridium rRNA group I (Clostridium sensu stricto), which includes Clostridium butyricum, the type species of the genus. The nearest phylogenetic relatives of the unknown bacterium corresponded to Clostridium absonum, Clostridium baratii, Eubacterium budayi, Eubacterium moniliforme, Eubacterium multiforme and Eubacterium nitritogenes, but 16S rRNA sequence divergence values of >3 % demonstrated that it represents a novel species. Based on the findings presented, a novel species, Clostridium colicanis sp. nov., is described, with the type strain 3WC2T (=CCUG 44556T =DSM 13634T).
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Lactobacillus thermotolerans sp. nov., a novel thermotolerant species isolated from chicken faeces
Five strains of thermotolerant lactic acid bacteria (G 12, G 22, G 35T, G 43 and G 44) isolated from chicken faeces were characterized taxonomically. The strains were facultatively anaerobic, Gram-positive, catalase-negative, non-motile, non-spore-forming rods. They were heterofermentative lactobacilli that produced dl-lactic acid. Growth of the strains occurred at 45 °C but not at 15 °C. The optimum temperature for growth was 42 °C, as determined from the specific growth rate. The highest permissive temperatures for growth were 50 °C for strain G 35T and 48 °C for the other four strains. DNA G+C content of the strains was between 49 and 51 mol%. Complex fatty acid patterns of the strains showed the presence of C14 : 0, C16 : 0, sometimes C18 : 0, C18 : 1 and C19 : 0 cyclo in the cell walls. Phylogenetic analysis of the 16S rRNA gene sequences of the five strains placed them in the Lactobacillus casei/Pediococcus group, with Lactobacillus fermentum as their closest relative (about 95 % sequence similarity). DNA–DNA hybridization data indicated that the thermotolerant strains were not L. fermentum. Taken together, the findings of this study show that the five strains isolated from chicken faeces represent a novel species within the genus Lactobacillus, for which the name Lactobacillus thermotolerans is proposed (G 35T =DSM 14792T =JCM 11425T).
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Streptomyces mexicanus sp. nov., a xylanolytic micro-organism isolated from soil
More LessThe taxonomic position of a thermophilic actinomycete strain isolated from soil was examined using a polyphasic approach. The strain, designated CH-M-1035T, was assigned to the genus Streptomyces on the basis of chemical and morphological criteria. It formed Rectiflexibiles aerial hyphae that carried long chains of rounded, smooth spores. The almost complete nucleotide sequence of the 16S rRNA gene of strain CH-M-1035T was determined and its comparison with the 16S rDNA sequences of previously studied streptomycetes confirmed the assignment of the novel strain to the genus Streptomyces. Strain CH-M-1035T clustered with species belonging to the Streptomyces thermodiastaticus clade in the 16S-rDNA-based phylogenetic tree. However, the phenotypic properties of strain CH-M-1035T differed from those of the recognized species within this clade. Therefore, it is proposed that strain CH-M-1035T be classified as a novel species within the genus Streptomyces, as Streptomyces mexicanus (type strain CH-M-1035T =DSM 41796T =BM-B-384T =NRRL B-24196T).
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Paenibacillus kribbensis sp. nov. and Paenibacillus terrae sp. nov., bioflocculants for efficient harvesting of algal cells
More LessTwo strains of Gram-variable, rod-shaped, endospore-forming, peritrichously flagellated, rod-shaped bacteria were isolated from a soil sample collected in Taejon City, Korea. The two strains (AM49T and AM141T) were found to be members of the genus Paenibacillus, on the basis of the results of phenotypic and phylogenetic analyses. Strains AM49T and AM141T were found to have a cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as their predominant menaquinone and anteiso-C15 : 0 as their major fatty acid. The DNA G+C contents of strains AM49T and AM141T were 48 and 47 mol%, respectively. The two strains formed distinct phylogenetic lineages within the radiation of the cluster comprising Paenibacillus spp. and a coherent cluster with Paenibacillus jamilae, Paenibacillus polymyxa, Paenibacillus azotofixans and Paenibacillus peoriae. The level of 16S rDNA similarity between strains AM49T and AM141T was 97·6 %, and 16S rDNA similarity values between strains AM49T and AM141T and the type strains of other Paenibacillus spp. ranged from 90·3 to 98·7 %. Levels of DNA–DNA similarity between the two strains and members of the genus Paenibacillus indicated that strains AM49T and AM141T were distinguishable from each other and from four phylogenetically related Paenibacillus spp. Therefore, on the basis of their phenotypic properties, phylogeny and genomic distinctiveness, it is proposed that strains AM49T and AM141T be placed in the genus Paenibacillus as two distinct novel species, Paenibacillus kribbensis (AM49T =KCTC 0766BPT =JCM 11465T) and Paenibacillus terrae (AM141T =KCCM 41557T =JCM 11466T).
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Agromyces aurantiacus sp. nov., isolated from a Chinese primeval forest
A catalase-negative actinomycete, strain YIM 21741T, was isolated from a soil sample collected from a primeval forest at Xishuangbanna, Yunnan Province, China. Analysis of 16S rDNA showed the strain to be related to members of the genus Agromyces, with which it also shares morphological characteristics, e.g. branching hyphae breaking into diphtheroid and rod-like, irregular, non-motile fragments and a peptidoglycan containing the diagnostic amino acid 2,4-diamino-n-butyric acid. Whole-cell hydrolysates of strain YIM 21741T contained rhamnose and small quantities of glucose, galactose and mannose. The major menaquinone was MK-12, while MK-13 and MK-12 were minor components. Diagnostic phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the DNA was 72·8 mol%. Physiological and biochemical characteristics reveal strain YIM 21741T to be different from all validly described species of the genus Agromyces. As DNA–DNA similarity values between this isolate and the phylogenetically neighbouring type strains of Agromyces bracchium and Agromyces luteolus are only moderate, the novel species Agromyces aurantiacus sp. nov. is proposed with strain YIM 21741T (=CCTCC 001012T =AS 4.1717T =DSM 14598T) as the type strain.
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Nocardiopsis xinjiangensis sp. nov., a halophilic actinomycete isolated from a saline soil sample in China
More LessAn actinomycete strain (YIM 90004T) was isolated from a saline soil sample from the Xinjiang Province, People's Republic of China. The strain displayed abundant aerial and substrate mycelia, and short spore chains were borne on the aerial mycelium. The spore chains were composed of non-motile, smooth-surfaced, rod-shaped spores. The cell wall of strain YIM 90004T contained mainly meso-diaminopimelic acid, alanine and glutamic acid (cell wall type III). Glucose, ribose, galactose, xylose and arabinose were the whole-cell sugars of the strain. The predominant phospholipids were phosphatidylinositol and phosphatidylglycerol; MK-10(H2) and MK-10(H4) were the predominant menaquinones. The DNA G+C content of strain YIM 90004T was 74·3 mol%. Chemotaxonomic properties and 16S rDNA analysis placed strain YIM 90004T in the genus Nocardiopsis. On the basis of phenotypic and phylogenetic analyses and DNA–DNA hybridization results, strain YIM 90004T (=CCRC 16285T =CCTCC AA99004T =DSM 44589T) is considered to represent a novel species of the genus Nocardiopsis, for which the name Nocardiopsis xinjiangensis is proposed.
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- Unicellular Eukaryotes
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Starmerella meliponinorum sp. nov., a novel ascomycetous yeast species associated with stingless bees
Thirty-two strains of the novel species Starmerella meliponinorum sp. nov. were isolated from various substrates associated with three stingless bee species (tribe Meliponini) in Brazil and one in Costa Rica. The strains were found in garbage pellets (faecal material, discarded pollen or food, etc.), pollen provisions, adult bees, honey and propolis of Tetragonisca angustula, in honey from Melipona quadrifasciata and in adults of Melipona rufiventris and Trigona fulviventris. The sequence of the D1/D2 domains of the large-subunit rDNA showed that the novel species belongs to the Starmerella clade and is most closely related to Candida etchellsii, although the two differ in their sequences by 7 % base substitutions. S. meliponinorum is homothallic and assimilates few carbon sources. Nitrate is utilized as a sole nitrogen source. The type strain of S. meliponinorum is strain UFMG-01-J26.1T (=CBS 9117T).
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Candida kunwiensis sp. nov., a yeast associated with flowers and bumblebees
More LessA novel asexual ascomycetous yeast, Candida kunwiensis (SG99-26T =KCTC 17041T =CBS 9067T), was isolated from sweet potato (Ipomoea batatas) flowers in Korea and from the body surface of pollinating bumblebees in Germany. Comparative analysis of the D1/D2 domain of 26S rDNA of all available sequences for ascomycetous yeasts showed that the novel species was phylogenetically related to the genus Metschnikowia, but the sequence similarity was low. Morphologically and physiologically, C. kunwiensis in many ways resembles Metschnikowia pulcherrima, but can be distinguished from this species by its ability to assimilate lactic acid and its inability to produce pulcherrimin.
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- Evolution, Phylogeny And Biodiversity
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Significant differences between Lactobacillus casei subsp. casei ATCC 393T and a commonly used plasmid-cured derivative revealed by a polyphasic study
More LessMany studies on Lactobacillus casei subsp. casei (L. casei) have been carried out using strain ATCC 393 (pLZ15−). Four strains of L. casei ATCC 393T and three of ATCC 393 (pLZ15−) were compared using phenotypic methods and many of the available genotyping techniques. These tests showed that strains of ATCC 393T obtained from independent public type-culture collections were significantly different from the plasmid-free (pLZ15−) strains of ATCC 393T. These findings were confirmed by sequencing the first 580 nt (domain I) of the 16S and 23S rDNAs of the strains. Complete sequencing of the 16S rDNA of one representative strain from each group revealed that strain ATCC 393T from culture collections was 99 % similar to Lactobacillus zeae ATCC 15820T and that the strain so far considered as L. casei ATCC 393 (pLZ15−) was, in turn, 100 % similar to L. casei ATCC 334 and Lactobacillus paracasei subsp. paracasei ATCC 4022. All data obtained in this work indicate that the ancestral strain of ATCC 393 (pLZ15−) might never have been the strain that is now available from culture collections.
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Phylogenetic study of Staphylococcus and Macrococcus species based on partial hsp60 gene sequences
More LessA 600 bp partial hsp60 gene sequence has been described previously as a novel genetic marker for species identification and phylogenetic studies within the genus Staphylococcus. In the present study, the 600 bp partial hsp60 gene sequences of 40 validly described Staphylococcus species and subspecies and four Macrococcus species were PCR-amplified and sequenced. Phylogenetic analysis revealed excellent concordance between the unrooted dendrograms based on partial hsp60 and 16S rRNA gene sequences. The genus Macrococcus is clearly separated from the genus Staphylococcus, but is closely related to the ‘sciuri group’, the only staphylococci that are cytochrome c oxidase-positive. The remaining Staphylococcus species clustered into five broad-based subdivisions, which corresponded to the ‘aureus group’, the ‘epidermidis group’, the ‘haemolyticus group’, the ‘saprophyticus group’ and the ‘intermedius group’. These results agreed remarkably well with the current taxonomy of this diverse family, which is based on classical phenotypic and biochemical testing. Furthermore, pairwise sequence comparisons indicated that the hsp60 gene is more divergent and more discriminatory than the 16S rRNA gene for species differentiation among strains of the genera Staphylococcus and Macrococcus. It is concluded that the hsp60 gene may be an efficient alternative target for taxonomic and phylogenetic studies on members of these genera.
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Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils
More LessVarious bacterial species in the genus Pasteuria have great potential as biocontrol agents against plant-parasitic nematodes, although study of this important genus is hampered by the current inability to cultivate Pasteuria species outside their host. To aid in the study of this genus, an extensive 16S rRNA gene sequence phylogeny was constructed and this information was used to develop cultivation-independent methods for detection of Pasteuria in soils and nematodes. Thirty new clones of Pasteuria 16S rRNA genes were obtained directly from nematodes and soil samples. These were sequenced and used to construct an extensive phylogeny of this genus. These sequences were divided into two deeply branching clades within the low-G+C, Gram-positive division; some sequences appear to represent novel species within the genus Pasteuria. In addition, a surprising degree of 16S rRNA gene sequence diversity was observed within what had previously been designated a single strain of Pasteuria penetrans (P-20). PCR primers specific to Pasteuria 16S rRNA for detection of Pasteuria in soils were also designed and evaluated. Detection limits for soil DNA were 100–10 000 Pasteuria endospores (g soil)−1.
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Phylogenetic heterogeneity of the species Acidithiobacillus ferrooxidans
Polyphasic genotypic analysis of 25 Acidithiobacillus ferrooxidans strains isolated from ores and ore concentrates collected in different regions of the world showed considerable strain heterogeneity. Restriction patterns of the chromosomal DNA of these strains obtained by PFGE were specific for each strain. According to the degree of DNA relatedness, 17 of the 23 strains studied were divided into four genomovars. Six independent, considerably divergent strains could not be assigned to any of the genomovars. A comparison of nearly complete nucleotide sequences of the 16S rDNA of five representatives of the genomovars (including the type strain of A. ferrooxidans, ATCC 23270T) with those of species of the genus Acidithiobacillus available from GenBank showed that most of the A. ferrooxidans strains, together with the type strain and some other strains of the species Acidithiobacillus thiooxidans, comprised a monophyletic cluster. Within this major cluster, A. ferrooxidans strains fell into four phylogenetic groups that were equidistant from the phylogenetic group of A. thiooxidans strains. In general, the distribution of strains among the phylogenetic groups correlated with their distribution among the genomovars, except that the representatives of two different genomovars fell into one phylogenetic group. Thus, at least two levels of phylogenetic heterogeneity for A. ferrooxidans have been found. The phylogenetic heterogeneity of A. ferrooxidans strains, which are phenotypically indistinguishable, suggests the occurrence of microevolutionary processes in different econiches. This should be taken into account in the biohydrometallurgical applications of A. ferrooxidans strains.
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Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases
More LessA significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.
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Phylogeny of gregarines (Apicomplexa) as inferred from small-subunit rDNA and β-tubulin
More LessGregarines are thought to be deep-branching apicomplexans. Accordingly, a robust inference of gregarine phylogeny is crucial to any interpretation of apicomplexan evolution, but molecular sequences from gregarines are restricted to a small number of small-subunit (SSU) rDNA sequences from derived taxa. This work examines the usefulness of SSU rDNA and β-tubulin sequences for inferring gregarine phylogeny. SSU rRNA genes from Lecudina (Mingazzini) sp., Monocystis agilis Stein, Leidyana migrator Clopton and Gregarina polymorpha Dufour, as well as the β-tubulin gene from Leidyana migrator, were sequenced. The results of phylogenetic analyses of alveolate taxa using both genes were consistent with an early origin of gregarines and the putative ‘sister’ relationship between gregarines and Cryptosporidium, but neither phylogeny was strongly supported. In addition, two SSU rDNA sequences from unidentified marine eukaryotes were found to branch among the gregarines: one was a sequence derived from the haemolymph parasite of the giant clam, Tridacna crocea, and the other was a sequence misattributed to the foraminiferan Ammonium beccarii. In all of our analyses, the SSU rDNA sequence from Colpodella sp. clustered weakly with the apicomplexans, which is consistent with ultrastructural data. Altogether, the exact position of gregarines with respect to Cryptosporidium and other apicomplexans remains to be confirmed, but the congruence of SSU rDNA and β-tubulin trees with one another and with morphological data does suggest that further sampling of molecular data will eventually put gregarine diversity into a phylogenetic context.
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Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage
More LessOxyrrhis marina and Perkinsus marinus are two alveolate species of key taxonomic position with respect to the divergence of apicomplexans and dinoflagellates. New sequences from Oxyrrhis, Perkinsus and a number of dinoflagellates were added to datasets of small-subunit (SSU) rRNA, actin, α-tubulin and β-tubulin sequences, as well as to a combined dataset of all three protein-coding genes, and phylogenetic trees were inferred. The parasitic Perkinsus marinus branches at the base of the dinoflagellate clade with high support in most of the individual gene trees and in the combined analysis, strongly confirming the position originally suggested in previous SSU rRNA and actin phylogenies. The SSU rRNA from Oxyrrhis marina is extremely divergent, and it typically branches with members of the Gonyaulacales, a dinoflagellate order where SSU rRNA sequences are also divergent. Conversely, none of the three protein-coding genes of Oxyrrhis is noticeably divergent and, in trees based on all three proteins individually and in combination, Oxyrrhis branches at the base of the dinoflagellate clade, typically with high bootstrap support. In some trees, Oxyrrhis and Perkinsus are sisters, but most analyses indicate that Perkinsus diverged prior to Oxyrrhis. Morphological characters have previously pointed to Oxyrrhis as an early branch in the dinoflagellate lineage; our data support this suggestion and significantly bolster the molecular data that support a relationship between Perkinsus and dinoflagellates. Together, these two organisms can be instrumental in reconstructing the early evolution of dinoflagellates and apicomplexans by helping to reveal aspects of the ancestors of both groups.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 16 (1966)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)